GapMind for Amino acid biosynthesis

 

Alignments for a candidate for fbp in Herbaspirillum seropedicae SmR1

Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate HSERO_RS03355 HSERO_RS03355 fructose-bisphosphate aldolase

Query= SwissProt::Q56815
         (354 letters)



>FitnessBrowser__HerbieS:HSERO_RS03355
          Length = 354

 Score =  521 bits (1343), Expect = e-153
 Identities = 262/353 (74%), Positives = 300/353 (84%)

Query: 1   MALVSMRQLLDHAADDSYGLPAFNVNNMEQVKAIMDAARATSSPVILQGSAGARKYAGEP 60
           M LVSMRQLLDHAA++ YGLPAFNVNN+EQV AIM+AA    +PVI+Q SAGARKYAGE 
Sbjct: 1   MPLVSMRQLLDHAAENGYGLPAFNVNNLEQVTAIMEAANEVGAPVIMQASAGARKYAGEA 60

Query: 61  FLRHLIAAAVEAYPEIPVVMHQDHGASPAVCMGAIKSGFSSVMMDGSLKEDGKTPADYDY 120
           FLRHLI+AAVEAYP IPVVMHQDHG SPAVCM AIKSGFSSVMMDGSL+ DGKT A Y+Y
Sbjct: 61  FLRHLISAAVEAYPHIPVVMHQDHGQSPAVCMAAIKSGFSSVMMDGSLEADGKTVASYEY 120

Query: 121 NVSVTAKVVELAHAVGVSVEGELGCLGSLETGKGEAEDGHGAEEALDHSKLLTDPDEAAQ 180
           NV V+ KVVE +HA+GV+VE ELG LGSLET KG+ EDGHGA+  +   +LLTD ++AA 
Sbjct: 121 NVEVSRKVVEFSHAIGVTVEAELGVLGSLETMKGDKEDGHGADGTMTREQLLTDVNQAAD 180

Query: 181 FVKATQCDALAIAIGTSHGAYKFTRKPTGDILAIDRIKAIHQRIPTTHLVMHGSSSVPQE 240
           FVKATQCDALAIAIGTSHGAYKF+RKPTGDILAIDRIK IH RIP THLVMHGSSSVPQE
Sbjct: 181 FVKATQCDALAIAIGTSHGAYKFSRKPTGDILAIDRIKEIHARIPNTHLVMHGSSSVPQE 240

Query: 241 LLEEIRTYGGDIKETYGVPVEEIQEGIRYGVRKVNIDTDIRLAMTAAIRRVGAKNKSEFD 300
           LL EIR +GGD+KETYGVPVEEIQEGI++GVRK+NIDTDIRLAMT AIRR   +N S+FD
Sbjct: 241 LLAEIREFGGDMKETYGVPVEEIQEGIKHGVRKINIDTDIRLAMTGAIRRYLFENPSKFD 300

Query: 301 PRKFMAAAMEEAKKVCIARFEAFGSAGKAEKIRAIELDEMAKRYASGELAQVV 353
           PR ++  A E AK VC ARF +FG  G+A KI+ I L+++A++Y SGELAQ+V
Sbjct: 301 PRDYLKPAREAAKLVCKARFLSFGCEGQAGKIKPISLEKIAEKYKSGELAQIV 353


Lambda     K      H
   0.316    0.132    0.369 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 463
Number of extensions: 14
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 354
Length of database: 354
Length adjustment: 29
Effective length of query: 325
Effective length of database: 325
Effective search space:   105625
Effective search space used:   105625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate HSERO_RS03355 HSERO_RS03355 (fructose-bisphosphate aldolase)
to HMM TIGR01521 (fba: fructose-bisphosphate aldolase, class II, Calvin cycle subtype (EC 4.1.2.13))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01521.hmm
# target sequence database:        /tmp/gapView.30432.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01521  [M=347]
Accession:   TIGR01521
Description: FruBisAldo_II_B: fructose-bisphosphate aldolase, class II, Calvin cycle subtype
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                  Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.1e-181  588.6   0.9   2.3e-181  588.4   0.9    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS03355  HSERO_RS03355 fructose-bisphosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS03355  HSERO_RS03355 fructose-bisphosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  588.4   0.9  2.3e-181  2.3e-181       1     347 []       3     349 ..       3     349 .. 1.00

  Alignments for each domain:
  == domain 1  score: 588.4 bits;  conditional E-value: 2.3e-181
                                  TIGR01521   1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaav 68 
                                                l+s+rqlldhaae+gyg+pafnvnnleq+ aimeaa++  +pvi+qas+gar+yage++lr+l+ aav
  lcl|FitnessBrowser__HerbieS:HSERO_RS03355   3 LVSMRQLLDHAAENGYGLPAFNVNNLEQVTAIMEAANEVGAPVIMQASAGARKYAGEAFLRHLISAAV 70 
                                                69****************************************************************** PP

                                  TIGR01521  69 eeypdipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgas 136
                                                e yp+ipvv+hqdhg+spa+c++ai+ gf+svmmdgsl++d+kt a+y+ynv+v+ +vv+++ha+g++
  lcl|FitnessBrowser__HerbieS:HSERO_RS03355  71 EAYPHIPVVMHQDHGQSPAVCMAAIKSGFSSVMMDGSLEADGKTVASYEYNVEVSRKVVEFSHAIGVT 138
                                                ******************************************************************** PP

                                  TIGR01521 137 vegelgclgsletgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrk 204
                                                ve elg lgslet kg++edghg++g++ r qlltd ++aa+fvk t+ dala+aigtshgaykf+rk
  lcl|FitnessBrowser__HerbieS:HSERO_RS03355 139 VEAELGVLGSLETMKGDKEDGHGADGTMTREQLLTDVNQAADFVKATQCDALAIAIGTSHGAYKFSRK 206
                                                ******************************************************************** PP

                                  TIGR01521 205 ptgevlaidrieeiherlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkv 272
                                                ptg++laidri+eih+r+p+thlvmhgsssvpqe l+ i e+gg++ketygvpveei++gik+gvrk+
  lcl|FitnessBrowser__HerbieS:HSERO_RS03355 207 PTGDILAIDRIKEIHARIPNTHLVMHGSSSVPQELLAEIREFGGDMKETYGVPVEEIQEGIKHGVRKI 274
                                                ******************************************************************** PP

                                  TIGR01521 273 nidtdlrlaataalrrvaakdpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemar 340
                                                nidtd rla+t+a+rr + ++ps+fdpr +lk+a ea k vckar+ +fg  g+a kik++sle++a+
  lcl|FitnessBrowser__HerbieS:HSERO_RS03355 275 NIDTDIRLAMTGAIRRYLFENPSKFDPRDYLKPAREAAKLVCKARFLSFGCEGQAGKIKPISLEKIAE 342
                                                ******************************************************************** PP

                                  TIGR01521 341 ryakgel 347
                                                +y +gel
  lcl|FitnessBrowser__HerbieS:HSERO_RS03355 343 KYKSGEL 349
                                                *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (347 nodes)
Target sequences:                          1  (354 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.48
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory